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Don't change the mapping quality of MQ=255 reads in IR

This commit is contained in:
Eric Banks 2011-11-05 22:40:45 -04:00
parent de07e06cbc
commit 90a053ea93
1 changed files with 2 additions and 1 deletions
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public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
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@ -817,7 +817,8 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
// For now, we will just arbitrarily add 10 to the mapping quality. [EB, 6/7/2010].
// TODO -- we need a better solution here
GATKSAMRecord read = aRead.getRead();
read.setMappingQuality(Math.min(aRead.getRead().getMappingQuality() + 10, 254));
if ( read.getMappingQuality() != 255 ) // 255 == Unknown, so don't modify it
read.setMappingQuality(Math.min(aRead.getRead().getMappingQuality() + 10, 254));
// before we fix the attribute tags we first need to make sure we have enough of the reference sequence
int neededBasesToLeft = leftmostIndex - read.getAlignmentStart();